Contacts of the strand formed by residues 179 - 183 (chain B) in PDB entry 2WWR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER 3.5 4.0 + - - -
155B THR* 3.4 29.3 - - + +
156B VAL 3.1 25.3 + - - +
177B VAL* 3.5 7.3 - - - +
178B GLN* 1.3 96.5 - - + +
180B PHE* 1.3 62.7 + - - +
181B LEU* 4.9 8.1 - - + +
198B GLU* 4.9 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 3.2 35.0 - - + -
158B ILE* 4.0 13.2 - - + -
169B ALA* 3.5 38.8 - - + -
172B LEU* 3.9 13.5 - - + -
173B LYS* 3.9 19.5 - - + -
177B VAL* 4.0 22.2 - - + -
178B GLN 6.0 0.4 - - - -
179B ARG* 1.3 74.0 - - - +
181B LEU* 1.3 67.4 + - - +
195B PHE* 3.6 41.2 + - + +
196B GLN 3.9 4.2 + - - +
197B ALA* 3.4 14.5 - - + -
198B GLU* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 3.7 28.0 - - + -
156B VAL 3.1 8.5 + - - +
157B GLY* 3.3 2.6 - - - -
158B ILE* 2.9 27.3 + - - +
179B ARG* 4.9 12.6 - - + +
180B PHE* 1.3 84.3 - - - +
182B TYR* 1.3 64.2 + - - +
197B ALA* 5.1 0.7 - - - -
198B GLU* 3.4 37.9 - - + +
200B VAL* 4.0 20.4 - - + -
204B GLU 4.8 0.7 - - - +
205B LEU* 4.1 12.3 - - + -
208B GLN* 4.0 21.1 - - + -
209B SER* 4.3 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE 3.2 14.4 - - - +
161B LEU* 3.7 40.4 - - + -
181B LEU* 1.3 76.0 - - - +
183B THR* 1.3 69.4 + - - +
186B GLN 4.6 3.4 - - - -
187B PRO* 3.4 13.5 - - + +
188B ARG* 2.9 37.7 + - + -
189B PRO* 4.5 1.2 - - - +
192B ALA* 3.9 9.5 - - + +
197B ALA* 3.5 28.3 - - + -
198B GLU 2.9 18.3 + - - +
199B PHE* 3.4 39.1 - + + +
200B VAL* 2.9 26.9 + - - +
205B LEU* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE 3.3 1.8 + - - -
159B ILE* 3.8 37.5 - - + +
160B GLY* 3.3 23.0 + - - -
161B LEU 4.5 0.3 + - - -
182B TYR* 1.3 83.6 - - - +
184B GLY* 1.3 65.0 + - - +
199B PHE* 3.8 9.5 - - - -
200B VAL 3.3 17.0 + - - -
201B SER* 4.8 0.4 - - - -
202B THR* 3.8 26.5 + - + +
205B LEU* 4.1 11.9 - - + -
225B LEU* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il